AquaLeap representatives from the University and industry outline their method for studying this pervasive disease.
21/1/2022
The AquaLeap consortium project is comprised of five teams, which combine university, government, and industry scientists. Each team pursues objectives related to advancing selective breeding in several UK aquaculture species. Since it began in January of 2019, some exciting progress has been made, and we are happy to provide some further updates.
The below report provides insight into ongoing research by the University of Edinburgh and external partners comprising one of the project’s five teams. Their study of the European flat oyster) aims to form a reference genome for the species, which will also support AquaLeap research into genetic resistance to the bonamia parasite.
A reference genome assembly for the European flat oyster
Report by Manu Kumar Gundappa (University of Edinburgh)
Here is a Hi-C contact map highlighting the 10 super scaffolds generated using HiRise™ scaffolding tool.
The European flat oyster (Ostrea edulis) is a key molluscan species widely distributed across the coasts of Europe. This species has been a part of the human diet for centuries and has recently been gaining prominence as an aquaculture species. However, multiple factors—including overexploitation and parasitic disease outbreaks—have seriously hindered production and threatened wild stocks over the last century. A high quality genome assembly is essential to realising the full potential of genetic tools towards reducing disease outbreaks and supporting stock restoration.
A high-quality reference genome has been generated by the AquaLeap team using a combination of various sequencing technologies. Long read sequencing on the Oxford Nanopore PromethION platform was used to generate a base assembly, which was polished using short read Illumina data. The resulting contigs were assembled into chromosome level scaffolds using a proximity ligation-based Omni-C technique. A RAD-seq based linkage map for flat oyster was generated in collaboration with Doctor Carolina Peñaloza and Professor Ross Houston (University of Edinburgh), in addition to Doctor Arnaud Tanguy (Roscoff Marine Station). The linkage map confirmed the ordering and orientation of scaffolds, leading to a high-quality chromosome scale reference genome. The final assembly was 935,138,052 base pairs long, with 93% contained in 10 “super scaffolds” corresponding to 10 chromosomes.
Here is a Circos plot demonstrating the congruence between the 10 super scaffolds of the flat oyster genome assembly and a new linkage map developed for this species. Sc1 to Sc10 indicate the ten super scaffolds of the genome assembly. LG1 to LG10 highlight the ten linkage groups corresponding to the ten chromosomes.
The finished assembly revealed a high gene completeness and comprised 56% repetitive sequence. Gene model prediction identified 35,699 protein-coding genes, corresponding well with predictions for existing bivalve genomes. The finished flat oyster genome assembly and annotation has been shared with researchers within and outside the AquaLeap consortium and was recently deposited to the NCBI database (set for public release in early 2022). We hope this effort will contribute to ongoing efforts to conserve and restore native flat oyster populations, and to reduce the prevalence of disease outbreaks via selective breeding.
